SHIP164 is a Chorein Motif Lipid Transfer Protein that Controls Endosome‐Golgi Membrane Traffic

Abstract

Recent studies have shown that proteins with an N‐terminal chorein motif are lipid transport proteins and further suggested that they mediate lipid transfer between closely apposed membranes by a novel bridge‐like mechanism. Within these proteins, the chorein motif represents the beginning of a rod‐like structure that harbors a hydrophobic groove running along its entire length. Lipids are thought to transfer between bilayers by sliding along this groove (PMID: 34216812). VPS13 and ATG2 are founding members of this family. Another protein with a predicted N‐terminal chorein motif is SHIP164 (UHRF1BP1L), previously identified as a Syntaxin 6‐binding protein (PMID: 20163565) and as a Parkinson’s Disease (PD) susceptibility candidate gene (PMID: 28137300). Here, we first explored whether the similarity of SHIP164 to VPS13 and ATG2 extends beyond the chorein domain and determined by cryo‐EM that SHIP164, like these two proteins, has an elongated hollow rod‐like structure. We also found that SHIP164 harbors glycerolipids in an aqueous environment and transports them between membrane bilayers in a liposome‐based assay. We further investigated the localization and physiological function of SHIP164 in mammalian cells. We found that endogenous SHIP164 is localized to cation‐independent mannose‐6‐phosphate receptor (MPR)‐positive vesicular structures at the cell periphery and that its over‐expression induces the abnormal formation of dynamic clusters of small 50‐70nm vesicles enriched in these receptors and anchored to endosomes. We also found that SHIP164 interacts with proteins implicated retrograde microtubule‐based transport from endosomes to the Golgi complex: the dynein/dynactin accessory factor LC8 and dynein interactor Rab45/RASEF. Accordingly, in SHIP164 knockout (KO) RPE‐1 cells, the traffic of MPR and Sortilin positive vesicles to the Golgi complex is partially impaired. An additional defect observed in SHIP164 KO cells is the absence of the largest endosomes positive for PI3P and EEA1. In view of the lipid harboring properties of SHIP164 it is tempting to speculate that the latter phenotype may be explained by its lipid transport properties that, as in the case of VPS13 and ATG2, may allow membrane expansion. Direct evidence for such a model is missing, although, we found that SHIP164 positive vesicles are also positive for ATG9, the autophagy factor recently found to function as a scramblase in partnership with ATG2 on autophagosome membranes. An attractive possibility is that SHIP164 may participate in the regulation of endocytic flow by acting in partnership with ATG9 in the control of phospholipids/protein ratio on the membranes of endocytic vesicles.